PDB-8zj7: Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in c...

ID or keywords:

Entry

Database: PDB / ID: 8zj7

Title

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-Dihydroxybenzoate and NAD.

Components

4-hydroxythreonine-4-phosphate dehydrogenase

Keywords

LYASE / Metal-dependent oxidative Decarboxylase / OXIDOREDUCTASE / Lyase.

Function / homology

4-hydroxythreonine-4-phosphate dehydrogenase / 4-hydroxythreonine-4-phosphate dehydrogenase activity / PdxA family / Pyridoxal phosphate biosynthetic protein PdxA / NAD binding / metal ion binding / 3,4-DIHYDROXYBENZOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-hydroxythreonine-4-phosphate dehydrogenase

Function and homology information

Biological species

Comamonas testosteroni KF-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Kumar, K.A. / Pahwa, D. / Kumar, P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-Dihydroxybenzoate and NAD.
Authors: Kumar, K.A. / Pahwa, D.

History

Deposition	May 14, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 25, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Derived calculations / Structure summary / Category: pdbx_entry_details / pdbx_struct_assembly_prop Item: _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly_prop.value

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zj7.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8zj7.ent.gz	770.7 KB	Display	PDB format
PDBx/mmJSON format	8zj7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8zj7_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	8zj7_full_validation.pdf.gz	2.7 MB	Display
Data in XML	8zj7_validation.xml.gz	50.6 KB	Display
Data in CIF	8zj7_validation.cif.gz	66.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zj/8zj7 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/8zj7	HTTPS FTP

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Related structure data

Related structure data	8zhy 8zi8 8zin 8zj0 8zj3 8zj5
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: 4-hydroxythreonine-4-phosphate dehydrogenase

C: 4-hydroxythreonine-4-phosphate dehydrogenase

D: 4-hydroxythreonine-4-phosphate dehydrogenase

A: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

135 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: 4-hydroxythreonine-4-phosphate dehydrogenase

D: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
67.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 4-hydroxythreonine-4-phosphate dehydrogenase

A: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

defined by author&software
67.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.303, 98.148, 168.036
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	B
3	2	B
4	2	B
5	3	B
6	3	B
7	4	B
8	4	B
9	5	B
10	5	B
11	6	B
12	6	B

NCS domain segments:

End auth comp-ID: GLN / End label comp-ID: GLN / Auth asym-ID: B / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	1 - 313	2 - 314
2	1	1	MET	MET	1 - 313	2 - 314
3	2	2	MET	MET	1 - 313	2 - 314
4	2	2	MET	MET	1 - 313	2 - 314
5	3	3	THR	THR	2 - 313	3 - 314
6	3	3	THR	THR	2 - 313	3 - 314
7	4	4	MET	MET	1 - 313	2 - 314
8	4	4	MET	MET	1 - 313	2 - 314
9	5	5	THR	THR	2 - 313	3 - 314
10	5	5	THR	THR	2 - 313	3 - 314
11	6	6	THR	THR	2 - 313	3 - 314
12	6	6	THR	THR	2 - 313	3 - 314

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules BCDA

#1: Protein	4-hydroxythreonine-4-phosphate dehydrogenase Mass: 33126.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Gene: CtesDRAFT_PD2128 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B7WRJ7, 4-hydroxythreonine-4-phosphate dehydrogenase

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Non-polymers , 7 types, 134 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID Mass: 154.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₇H₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density meas: 0.36 Mg/m³ / Density % sol: 54.98 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2 M Potassium sodium tartrate tetrahydrate 20% w/v Polyethylene glycol 3,350 pH 7.4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 13, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.885 Å / Relative weight: 1
Reflection	Resolution: 2.26→168 Å / Num. obs: 42519 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.116 / R_pim(I) all: 0.052 / R_rim(I) all: 0.127 / Net I/σ(I): 10.5
Reflection shell	Resolution: 2.26→2.3 Å / R_merge(I) obs: 1.257 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3343 / CC_1/2: 0.624 / R_pim(I) all: 0.543 / R_rim(I) all: 1.372 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
autoPROC		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→24.001 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.921 / SU B: 34.187 / SU ML: 0.297 / Cross valid method: FREE R-VALUE / ESU R Free: 0.328
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2517	2135	5.021 %
R_work	0.1813	40384	-
all	0.185	-	-
obs	-	42519	99.548 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 49.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.9 Å²	0 Å²	0 Å²
2-	-	11.944 Å²	-0 Å²
3-	-	-	-5.044 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→24.001 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9182	0	128	122	9432

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	9458
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9231
X-RAY DIFFRACTION	r_angle_refined_deg	1.502	1.802	12885
X-RAY DIFFRACTION	r_angle_other_deg	0.49	1.723	21215
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.997	5	1247
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.795	5	61
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.763	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.016	10	1530
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.626	10	348
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1560
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11101
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1933
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	1791
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	8112
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	4640
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	5167
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.186	0.2	188
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.266	0.2	4
X-RAY DIFFRACTION	r_metal_ion_refined	0.035	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.239	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.16	0.2	83
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.4	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	11.088	4.702	5003
X-RAY DIFFRACTION	r_mcbond_other	11.086	4.702	5003
X-RAY DIFFRACTION	r_mcangle_it	16.897	8.462	6245
X-RAY DIFFRACTION	r_mcangle_other	16.896	8.463	6246
X-RAY DIFFRACTION	r_scbond_it	13.065	5.287	4455
X-RAY DIFFRACTION	r_scbond_other	13.057	5.287	4454
X-RAY DIFFRACTION	r_scangle_it	19.689	9.518	6640
X-RAY DIFFRACTION	r_scangle_other	19.683	9.518	6640
X-RAY DIFFRACTION	r_lrange_it	49.141	45.244	9843
X-RAY DIFFRACTION	r_lrange_other	48.092	45.21	9838
X-RAY DIFFRACTION	r_rigid_bond_restr	5.594	3	18689
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.096	0.05	8935
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.093	0.05	8884
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.097	0.05	8973
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.089	0.05	8877
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.099	0.05	8904
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.094	0.05	8907

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	B	X-RAY DIFFRACTION	Local ncs	0.09559	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.09559	0.05009
2	3	B	X-RAY DIFFRACTION	Local ncs	0.09299	0.05009
2	4	B	X-RAY DIFFRACTION	Local ncs	0.09299	0.05009
3	5	B	X-RAY DIFFRACTION	Local ncs	0.09712	0.05009
3	6	B	X-RAY DIFFRACTION	Local ncs	0.09712	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.08927	0.05009
4	8	B	X-RAY DIFFRACTION	Local ncs	0.08927	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.09921	0.05008
5	10	B	X-RAY DIFFRACTION	Local ncs	0.09921	0.05008
6	11	B	X-RAY DIFFRACTION	Local ncs	0.09375	0.05009
6	12	B	X-RAY DIFFRACTION	Local ncs	0.09375	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.65-2.718	0.319	151	0.277	2908	0.279	3063	0.93	0.967	99.8694	0.261
2.718-2.791	0.318	143	0.258	2855	0.261	2998	0.94	0.976	100	0.245
2.791-2.871	0.301	141	0.227	2763	0.231	2907	0.947	0.985	99.8968	0.217
2.871-2.958	0.303	154	0.207	2694	0.212	2849	0.934	0.987	99.9649	0.195
2.958-3.054	0.309	136	0.196	2627	0.201	2765	0.939	0.987	99.9277	0.184
3.054-3.159	0.312	144	0.204	2500	0.209	2649	0.921	0.982	99.8112	0.193
3.159-3.276	0.252	131	0.197	2474	0.2	2609	0.951	0.983	99.8467	0.187
3.276-3.407	0.267	123	0.183	2348	0.188	2472	0.958	0.984	99.9595	0.179
3.407-3.556	0.258	121	0.181	2265	0.185	2392	0.948	0.979	99.7492	0.177
3.556-3.725	0.257	109	0.169	2178	0.173	2296	0.95	0.985	99.608	0.171
3.725-3.921	0.278	99	0.174	2083	0.178	2196	0.948	0.983	99.3625	0.179
3.921-4.152	0.248	95	0.153	1969	0.158	2078	0.964	0.986	99.3263	0.166
4.152-4.429	0.179	96	0.131	1870	0.134	1973	0.982	0.991	99.6452	0.151
4.429-4.771	0.184	94	0.131	1728	0.134	1830	0.982	0.992	99.5628	0.157
4.771-5.206	0.236	87	0.147	1623	0.151	1715	0.973	0.99	99.7085	0.173
5.206-5.786	0.232	86	0.161	1479	0.165	1571	0.978	0.991	99.6181	0.187
5.786-6.617	0.261	87	0.166	1285	0.172	1382	0.956	0.985	99.2764	0.196
6.617-7.955	0.243	45	0.164	1171	0.167	1224	0.964	0.984	99.3464	0.198
7.955-10.679	0.176	56	0.184	921	0.184	983	0.989	0.99	99.3896	0.206
10.679-24.001	0.315	37	0.297	635	0.298	675	0.973	0.969	99.5556	0.314

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